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cryo2go
เข้าร่วมเมื่อ 17 พ.ย. 2011
TODO
Why do small image features end up outside the particle in Transmission Electron Microscopy images?
TEMs, like other microscopes are imperfect, and those imperfections blur any images. We describe the blurring by the point spread function, sometimes called the optical transfer function. In TEM, the PSF pushes finer image features further out of the particle than coarser features, and this effect is amplified the further from focus that we image. Why? Here is a quick hand-wavy explanation.
มุมมอง: 49
วีดีโอ
cisTEM_docs pt 1 - useful programs
มุมมอง 4022 ปีที่แล้ว
In addition to a nice single particle cryo-EM GUI, cisTEM also comes with programs that you may find useful in your own data analysis. cisTEM vs 1.0 beta (discussed in this video) has ~40 of these programs that can be used to do things like, calculate an FSC, resize a volume, change a volumes pixel size and so on. In this video I introduce documentation that describes reference material for the...
Paramter description
มุมมอง 5386 ปีที่แล้ว
Some details about each of the parameters needed for the introductory portion of the tutorial.
template matching - editing the results
มุมมอง 1.1K7 ปีที่แล้ว
Using the real space image, cummulative convolution map, and 3d model, rapidly edit template matching results.
inital Average and Alignment
มุมมอง 1.1K7 ปีที่แล้ว
create the project subTomoMeta, which is the binary file tracking the project, create and in initial average, evaluate FSC to confirm gold-standard compliance and final check on the average from each tomo to ensure quality. Set-up and run alignment.
template matching - setup and running
มุมมอง 1.1K7 ปีที่แล้ว
select a template, scale as necessary and define relevant parameters to find the initial coordinates and euler angles for the subtomograms in your sample.
selecting sub-areas for reconstruction
มุมมอง 9627 ปีที่แล้ว
Limits in x,y,z for each sub area are needed by emClarity for reconstructing tomograms as needed during subTomogram processing. Using this script makes defining those boundaries straightforward, and also provides an initial survey of the quality of the data.
emClarity tutorial - 2 - initial CTF estimation
มุมมอง 1.5K7 ปีที่แล้ว
an initial estimate of the ctf provides a good measure of the quality of each given data set, and will be necessary to move on after template matching. This also creates a copy of the aligned stack to be used for initial tomogram reconstructions.
emClarity tutorial - 1 - coarse alignment
มุมมอง 2.7K7 ปีที่แล้ว
After obtaining the tutorial data (or your own data later on) and setting up your project directory the next step is to estimate the tilt-series geometry and also obtain a model describing the location of any gold-fiducial markers to later be erased.
information on emClarity
มุมมอง 1.1K7 ปีที่แล้ว
describes where and how to find information to use gpu accelerated software for the enhanced macromolecular classification and alignment for high-resolution in situ tomography.
Rapidly fitting a PDB into and EM density prior to MDFF
มุมมอง 7K7 ปีที่แล้ว
Fitting a PDB into an EM density should be rapid and easy. This is one way to make that happen. Edits: Around 3:30 the affine transform in Chimera's results dialog is obviously 4x4 not 4x1 as I mis-stated. Also the translational displacement is in Angstroms, not in pixels.
thx for ur useful development, docs and podcasts!!!
THANKS!It's very helpful!
THANKS!It's very helpful!
Greatly appreciate video tutorials!
Great thanks Ben! it is really helpful!